One thing I liked about the Iron Man movies, compared to the original comic book source material, is that they make more of an effort to root themselves in the real world while still bringing along the fantastic. In the four-color comics, people throwing cars around the street is so commonplace that we focus almost entirely on the epic-scale battles between these vastly superpowered beings, with "normals" being barely more than set dressing and suitably vulnerable tokens of value to be fought over.
Tony Stark (the movie version) lives in a world that is much like ours, and reacts like ours would, but in which a very few people do some very amazing things -- amazing, but also explicable, even feasible. Yes, there are no arc reactors; but if there were a news article tomorrow about how Stephen Hawking, or the people at CERN, or even Google, had a breakthrough in energy technology, you would not conclude you were being pranked. Tony Stark's world reacts to him the way we would.
And Tony Stark's world is not (yet!) full of a dozen equally amazing and entirely unrelated origins for fantastic things. As of the end of the second movie, all the events which are beyond what our world expects are all consequences of the same set of scientific and technological advances created by a few geniuses, and a lot of people being extremely well trained in things people can actually do (Black Widow's martial arts may be better than anything you or I can imagine doing, but it's not significantly farther beyond an Olympic athlete than Tony's engineering is beyond the stuff they're doing at Sony).
We get a similar effect from the recent Batman movies, especially The Dark Knight, where the biggest plausabilty issues we have to face are logistical issues of how the villains find henchmen and funding, more than how there can be so many odd origins for "supers". Even the much-disliked Daredevil movie, which posited one almost-"supernatural" origin story for one character (but left everyone else simply "the best humans can be") stuck to a real world setting. (Its sequel, Elektra, cast that aside without realizing what it was giving up, more's the pity.)
I've always found the spandex-cape four-color version of the superhero genre a little harder to swallow, and most entertaining when it's being spoofed (as in The Incredibles or Mystery Men). It can be palatable if you provide a reason why, fairly recently, a world without "superpowers" suddenly got some, so everyone's origin stories are related, and there's a good reason why the world hasn't had a chance to react to the world-changing nature of this event by, well, changing the way it would. But if a superhero story isn't going to have that, it should just leap into its story and try to avoid dwelling on the oddity that simultaneously a bunch of people independently found amazing powers, but the world around them still remains familiar.
So as much as I've enjoyed Iron Man's recent incarnation in the movies, I'm nervous about the Avengers storyline that's clearly coming. I never read the comics, and frankly, always found the idea of Iron Man and Thor being on the same team as kind of incomprehensible, the sort of thing that works only because the writers keep the story moving too fast for anyone to stop and say WTF? But the comics-movies are heading that way.
The various Marvel-comic-based movies are all so far being treated like they're in their own universes, so no one needs to say, "wait, in one place someone's made a giant green monster with radiation and in another, someone's built a super-suit... why not get these guys together!" There's been a few tiny hints otherwise, but they're so small, things like news reports on screens in the background of shots, that you can easily ignore them. But once they change that and make it official that the Hulk and Iron Man are in the same world, things start getting wobbly. Throw Captain America and Magneto and Spiderman and the X-Men into that world, and all the previous movies start making no sense retroactively -- how could the events of any one of them not have been impacted by the existence of the others in that same world? Then, toss in an ancient Norse god, and all bets are off.
They could try to explain away all those questions, but that would likely create a big hairy pile of boring exposition that wouldn't really satisfy me, but would also drain the fun out of the movie. Or they could just strap us into the roller coaster and hope to keep us moving so fast we never got around to caring, which is the better approach, but I suspect it's still going to keep the movies from being as fun -- particularly on repeat views -- as the ones we've already had.
Maybe I'm wrong. Maybe the Avengers movie is going to be great. But I think for me, at least, the best of the comic book movies have happened, and we're on the edge of a transition into a new era of comic book movies that will be flashier and full of more gee-whiz but ultimately less satisfying and less enduring.